Molecular modelers often face an underappreciated challenge: keeping track of numerous molecules, scripts, conformations, and structure files within a growing project. As the complexity of a molecular simulation increases, so does the burden of managing its components. A cluttered workspace can lead to inefficiencies, errors, or even lost data.
If this sounds familiar, the folder system in SAMSON may be just what you need. SAMSON, the integrative molecular design platform, allows users to organize nodes—including molecules, files, and more—using an intuitive folder structure within documents. This feature can help you group related items, apply actions to multiple items collectively, and even simplify file sharing. Here’s how it works.
Why Use Folders?
Folders in SAMSON serve as containers for any type of node—atoms, molecules, images, scripts, even embedded files. You can think of folders as logical labels inside your document, helping to:
- Group related molecules for a specific study or experiment
- Quickly hide or show multiple nodes with one click
- Move or copy complete sets of nodes across documents
- Separate working regions without creating new documents
This means you no longer need to scroll through a long list of nodes to manage your project. Instead, simply collapse folders, just like in a file browser, to make navigation easier.
Creating a Folder
To create a folder within your document, go to the top menu and select Edit > Folder. This opens a new folder which you can rename and populate with any nodes of your choice by dragging them into it in the Document view.
Folders Are Self-Contained
Folders in SAMSON documents are not just visual organizers—they’re actually embedded in the document itself. That means when you save or share a document, all files and folders inside it go along for the ride. Whether you’re transferring a project between computers or collaborating with a colleague, you can be confident that no linked files get left behind.
This self-contained nature is especially useful when working with large simulation datasets, annotated images, PDFs, or companion Python scripts that support your modeling workflow.
A Practical Example
Say you’re designing a molecule that binds to a specific protein site. You could create a folder for the candidate structures, another for experimental data files, and a third for visual materials to include in a report. If you need to share your findings, simply send the SAMSON document—no need to package files individually.
Take Away Complexity
By using folders, you keep your workspace uncluttered and intuitive. You also reduce the risk of misplacing or misapplying operations, since folder hierarchies allow grouping-based selections and actions. This improves not only your efficiency but also the reproducibility of your molecular modeling work.
To learn more about using folders and documents in SAMSON, visit the original documentation page at https://documentation.samson-connect.net/users/latest/documents/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.